Beyond Tokens: Probing Higher-Order Epistasis in Learned Protein Representations

arXiv:2608.24953 · q-bio.QM, cs.LG · Submitted 2026-08-24 · Read on arXiv

q-bio.QM, cs.LG

Submitted: 2026-08-24

Updated: 2026-08-24

Comments: 32 pages, 4 figures, 10 tables

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Tokenization — 13× in this paper · explained in 2 episodes
• Benchmark — 12× in this paper · explained in 2 episodes
• Generalization — 9× in this paper · explained in 13 episodes
• Ablation — 6× in this paper · explained in 1 episode
• Regularization — 5× in this paper · explained in 3 episodes
• Residual Interaction Tokenization — 5× in this paper
• Benchmarking — 4× in this paper · explained in 4 episodes
• Provenance — 4× in this paper · explained in 4 episodes
• Transformer — 2× in this paper · explained in 2 episodes
• Accuracy — 1× in this paper · explained in 1 episode
• Adaptation — 1× in this paper · explained in 1 episode
• Generative AI — 1× in this paper · explained in 2 episodes
• Hamming Distance — 1× in this paper · explained in 2 episodes
• Representation Learning — 1× in this paper · explained in 2 episodes
• Spectral Geometry — 1× in this paper · explained in 2 episodes
• Trace — 1× in this paper · explained in 2 episodes
• alpha — 1× in this paper · explained in 1 episode

Sources

• BRIDGE: Bottleneck-Aware Regulator-Set Inference and Diagnosis for Cooperative Gene Regulatory Recovery

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